BioC 2.14: CHECK report for spliceSites on petty

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch spliceSites_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/spliceSites.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spliceSites/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spliceSites’ version ‘1.2.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘rbamtools’ ‘refGenome’ ‘doBy’ ‘Biobase’ ‘Biostrings’ ‘seqLogo’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘spliceSites’ can be installed ... [38s/40s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'readCuffGeneFpkm':
readCuffGeneFpkm
  Code: function(cuff, phenoData, summ = "max")
  Docs: function(cuff, phenoData)
  Argument names in code not in docs:
    summ

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [26s/26s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/spliceSites.Rcheck/00check.log’
for details.

* installing *source* package ‘spliceSites’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c spliceSites.c -o spliceSites.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o spliceSites.so spliceSites.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/spliceSites.Rcheck/spliceSites/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (spliceSites)

name	user	system	elapsed
SpliceCountSet-class	0.000	0.001	0.001
aaGapSites-class	0.492	0.021	0.538
addGeneAlignPart	0.543	0.005	0.548
addHbond	0.564	0.020	0.587
addMaxEnt	0.965	0.013	0.977
alt_X_ranks	0.035	0.002	0.037
annGapSites-class	0.166	0.007	0.173
annotate-ExpressionSet	0.329	0.019	0.348
annotation	0.091	0.004	0.094
cRanges-class	0.091	0.005	0.097
caRanges-class	0.215	0.005	0.221
cdRanges-class	1.440	0.155	1.599
countByGeneName	0.149	0.005	0.155
dnaGapSites-class	0.565	0.029	0.596
dnaRanges	0.884	0.019	0.909
extractByGeneName	0.426	0.007	0.432
extractRange	0.055	0.004	0.059
gapSites-class	0.096	0.006	0.101
gapSites	0.276	0.007	0.283
getGapSites	0.110	0.004	0.113
hbond-class	0.018	0.001	0.021
keyProfiler-class	0.040	0.002	0.042
lrCodons	0.074	0.002	0.077
maxEnt-class	0.035	0.005	0.040
rangeByGeneName	0.069	0.003	0.073
readCuffGeneFpkm	0.143	0.004	0.147
readExpSet	0.204	0.006	0.210
readMergedBamGaps	0.049	0.003	0.051
readTabledBamGaps	0.121	0.004	0.126
silic_tryp	0.004	0.001	0.005
spliceSites-package	0.134	0.008	0.143
trim	0.071	0.005	0.075
truncateSeq	0.169	0.005	0.173
truncate_seq	0.005	0.000	0.004
trypsinCleave	0.201	0.006	0.208
uniqueJuncAnn	0.227	0.004	0.232
write.files	0.165	0.003	0.169
xCodons	0.057	0.005	0.061
xJunc	0.067	0.003	0.070
xJuncStrand	0.057	0.003	0.059

BioC 2.14: CHECK report for spliceSites on petty

Summary

Command output